Question: how can i get p value from miRNA raw readcounts
0
gravatar for husainbioinfos
6 weeks ago by
pune
husainbioinfos0 wrote:

...working on lung cancer project and need to find out which genes are deferentially expressed and which are not. for that i a have downloaded miRNA data set from GEO id is GSE110907. And the file i got has to variable gene_id and read counts. from that i have to derive p value from that data/file.

example: input file :

id read_count hsa-miR-100-3p 568 hsa-miR-100-5p 176883 hsa-miR-101-3p 122968 hsa-miR-101-5p 923

output file: id read_count p value hsa-miR-100-3p 568 ? hsa-miR-100-5p 176883 ? hsa-miR-101-3p 122968 ? hsa-miR-101-5p 923 ?

rna-seq p value R • 254 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by husainbioinfos0

You need to give us more information. A p-value is associated to a certain hypothesis/test. What are you testing here?

What are you interested in knowing using the read counts? If you have multiple samples, you could compute a differential expression analysis where your miRNAs would have a p-value based on the method you used (limma for example.)

ADD REPLYlink written 6 weeks ago by manuel.belmadani1.2k

i want to perform deferentially expression of genes and want to derive p value.i have file which has miRNA id and read counts. how can i derived p value from miRNA id and read counts ? please explain

ADD REPLYlink written 6 weeks ago by husainbioinfos0
1

It really depend what's you're looking for, and what your data's like. Get an idea of what others have done first and what kind of tools they used, I find that's usually the best approach to figure it out. A good starting point would be to find some existing miRNA DE pipeline.

Some links to get you started:
https://github.com/bcgsc/mirna
miRNA differential expression
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1601-4
https://www.researchgate.net/post/Pipeline_for_miRNA_differential_expression_analysis_from_NGS_data2

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by manuel.belmadani1.2k

let me clarify...working on lung cancer project and need to find out which genes are deferentially expressed and which are not. for that i a have downloaded miRNA data set from GEO id is GSE110907. And the file i got has to variable gene_id and read counts. from that i have to derive p value from that data/file.

example:

input file :

id              read_count
hsa-miR-100-3p  568
hsa-miR-100-5p  176883
hsa-miR-101-3p  122968
hsa-miR-101-5p  923

output file:

id              read_count          p value
hsa-miR-100-3p  568                 ?
hsa-miR-100-5p  176883              ?
hsa-miR-101-3p  122968              ?
hsa-miR-101-5p  923                 ?
ADD REPLYlink modified 6 weeks ago by RamRS25k • written 6 weeks ago by husainbioinfos0

husainbioinfos : Please edit your original post to add more/new information.

SUBMIT ANSWER is for new answers to original question.

ADD REPLYlink written 6 weeks ago by genomax78k
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